How to use the centerline extractor?

[revygabor]

Hi!

I try to use the CenterlineExtraction class, but I can't make it work. Can you help me with that? My current code is:

import fast

fast.downloadTestDataIfNotExists()


importer = fast.ImageFileImporter.create(fast.Config.getTestDataPath() + 'retina.png')
centerline_extractor = fast.CenterlineExtraction.create().connect(importer)

res = centerline_extractor.runAndGetOutputData()

However it results in a mesh containing 0 vertices. What am I doing wrong?

Thank you for the help!

[smistad]

Hi

Unfortunately CenterlineExtraction is for 3D only as stated here: https://fast.eriksmistad.no/classfast_1_1CenterlineExtraction.html

You can try the skeletonization instead: https://fast.eriksmistad.no/classfast_1_1Skeletonization.html
It will however, only give you skeleton image, not a contour/mesh.

Here is a working example:

import fast

fast.downloadTestDataIfNotExists()

importer = fast.ImageFileImporter.create(fast.Config.getTestDataPath() + 'retina.png')
segment = fast.BinaryThresholding.create(100).connect(importer)
skeletonize = fast.Skeletonization.create().connect(segment)
renderer = fast.SegmentationRenderer.create().connect(skeletonize)
fast.SimpleWindow2D.create().connect(renderer).run()

It will give you this:

[revygabor]

Thank you for the quick answer! My original aim is to produce a centerline from a 3D binary mask. I attach a sample input.
vessel_mask.zip (0-1 unint8 values)

And my code is:
from scipy.io import loadmat
numpy_image = loadmat('vessel_mask.mat')['vessel_mask']

import fast
fast_image = fast.Image.createFromArray(numpy_image)
centerline_extractor = fast.CenterlineExtraction.create().connect(fast_image)
res = centerline_extractor.runAndGetOutputData()

However it doesn't give any result, but crashes the google colab session without any errors.
Could the colab environment or the code be the problem?

[smistad]

It seems the algorithm encounters an error with speed = 0 (some edge case maybe?).
I removed the check, and then it produces an output after a while:

[revygabor]

wow, thank you!
so, now I should just find the error, I guess :)

[smistad]

I removed the exit line when it encounters speed = 0, so that you can try it yourself. But you have to download and install a new wheel from here when its done: https://github.com/smistad/FAST/actions/runs/6720804256

[revygabor]

thank you very much!